The Kotomine Gene
by Sheo Darren
Summary: Blood runs thicker than water. The Fourth Grail War is nigh. This is the start of darkness for Kyouko, daughter of Kirei Kotomine, bearer of his gene.


If you somehow find her, if you dare to press her on the matter, and if you somehow survive her possibly violent response, Homura Akemi might deign to educate you about the existence of many, many timelines.

Not countless, contrary to what one might immediately think. The looper has kept accurate count of all her temporal back-steps, and her recollection remains crystal clear despite failure after abject failure that would cloud any other mind with black doubt and red haze.

Throughout her travels backward and forward through time and space, she has discovered that there are laws of time. Fixed points. Patterns in the tapestry of Fate. Outcomes that seemed predetermined no matter what one did.

One plus one equals two. Red and blue combine to form magenta. People die when they are killed.

Sayaka Miki will become a Witch and die if she contracts with Kyubey. Mami Tomoe will die in battle against Charlotte. Kyouko Sakura will die before Walpurgis Nacht arrives. And Madoka Kaname…

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**"Oh, Madoka…"**

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There are, of course, aberrations, exceptions that only serve to prove the rule. For example, in one timeline, Mami survived her encounter with Charlotte. She reunited with Kyouko, who was now allied with an orphan girl named Yuma Chitose.

That timeline remained a dead end. Madoka was murdered by Oriko Mikuni using a shard of the Witch that once was Kirika Kure. Homura herself came close to dying that time. Thereafter, she made it a priority goal to… remove Oriko and Kirika from the equation before they ever contracted with Kyubey.

.

"**Why? Why did you kill Kirika? Why are you going to kill me? Why?"**

"**I will save Madoka Kaname. No matter what."**

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In another timeline, Mami saved a young girl from a Witch. Inspired by her savior, Kazusa Michiru contracted with Kyubey. Kazusa fought the good fight as a magical girl and eventually met the better of the only two ends of all magical girls, dying in battle against a Witch in defense of the ones she loved.

There are deaths, and there are deaths. And for some, death is only the beginning. So it was with Kazusa.

Her friends, the so-called Pleiades Saints, could not accept her death, for what was it but proof of their own doom? They desperately sought a way to bring their heroine back to life by experimenting on Kazusa's corpse and the Soul Gems of captured Puella Magi. Their labors bore bitter fruit in the form of the thirteen clones, all named Kazumi, the last of whom became the Innocent Malice, the poppet who wished to become human- and achieved her dream through faith and sacrifice.

But Homura did not know of Kazumi. The clone was restricted to Asunaro City while the time traveler haunted Mitakihara City.

Homura's attention was totally devoted elsewhere. Not a Kaname? Not important.

(The distinction of being a Kaname is critical, by the way. Once, in her single-minded zeal to save the one she loved, Homura had disregarded the state of Madoka's family. The time traveler quickly discovered the fastest way to unleash Kriemhild Gretchen upon the world.)

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"**Mom… Dad… Tatsuya… I… I…"**

"**KYUUUBEEEY!"**

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It is one of those aberrant and ignored timelines that comes to fore in this tale. And like many other stories, it begins with a mother and her child.

In the prime timeline, the woman who married the Anglican priest Father Sakura and mothered Kyouko and Momo died by the hands of a husband whose brittle mind utterly broke when he learned that his eldest child had made a deal with the white devil.

In this timeline, Kyouko's mother contracted a terminal disease while pregnant with her second daughter. She miscarried, was devastated by the loss of the babe who would have born the name Momo, and never truly recovered.

On her deathbed, she begged her stoic husband, who in this timeline was probably the last and worst person possible.

"Dear, I know you cannot feel love for anything," she wheezed in a voice like sandpaper. "But could you at least try to act like a father to Kyouko?"

"I cannot," he automatically responded, subsumed in his personal sea of nihilistic emptiness whose depths none other could brave or stand for long.

But Kyouko's mother knew of such a chink in his armor. And she threw down the irresistible gauntlet.

"Are you saying you are no better than Gendo Ikari?"

Her husband's gaze flickered towards the survivors of the Ikari family. The widower Gendo was shoving a bass into the hands of his son Shinji. Said 'gift' was the fish, not the string instrument.

"This is the last thing I will do for you as your father," the bespectacled man dismissed.

Then, as if Gendo could feel the gaze on his back, he turned to smirk at his soon-to-be-fellow widower, as if daring him to outdo him.

Bushy black eyebrows, part of the family's sorcery trait, twitched at the affront/challenge. "I changed my mind," he suddenly declared to his wife. "I'll do it."

Yes. Even someone as morally maladjusted as Kirei Kotomine had standards.

Missus Kotomine smirked. Just as planned.

And the bleak future prompted by Fimbu1vetr's wishful review now reveals itself in…

.

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><p><strong>The Kotomine Gene<strong>

A Puella Magi Madoka Magica x Fate/Zero Story

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**Disclaimer:** Sheo Darren does not own Madoka, Fate, or the various franchises making an appearance in this story.

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><p>.<p>

Years later…

"Don't worry, my boy," Risei Kotomine assured his bleak-faced son. "I'll take good care of Kyouko-chan."

Their discussion was disrupted by the booming notes of Dies Irae thundering throughout the dim interior of the Fuyuki Church, where father and son had been transferred shortly after the death of Kirei's wife.

They looked to the pipe organ, where the youngest Kotomine was hammering out the foreboding tune with clumsy gusto.

"Nothing will happen to her," Risei added. "I promise."

.

The telephone is a privilege, not a right. It applies doubly so for magical telephones that your grandfather uses to communicate with his ally.

Unfortunately for G.I. Joe, Kyouko had rooted for COBRA from the very beginning.

"Hello, this is the Tohsaka residence," came the small voice that was way too serious.

Kyouko was barely able to stifle her laughter as she began the classic phone prank. "Is your refrigerator running?"

On the other end of the line, Rin Tohsaka frowned. "What's a refrigerator?" she asked.

The innocent question instantly derailed Kyouko's mischievous train of thought. "Don't you know what a refrigerator is?" she exclaimed.

"No. We don't have that. So what is it?"

"It's an appliance that keeps food and drinks cool," Kyouko explained, aghast at how technologically backwards the typical mage proved to be. Thank goodness she was part of the Church and not the Clock Tower!

"Oh, so it's an icebox," Rin realized from the description of its purpose. "Why didn't you say so immediately?"

It was Kyouko's turn to be confused. "What's an icebox?" she asked.

Incidentally, this was the very first time Rin used one of her sexy, sexy lecture poses.

From that day on, the Kotomine and Tohsaka heirs got along like Fuyuki City on hellfire. And like their fathers before them, their relationship could only end in a stabbing.

.

Risei proved true to his word. When the greedy Kayneth Archibald el-Melloi broke into the church to extort the promised reward of a command seal –and deny the rest to his rivals-, the elder Kotomine hid his granddaughter in one of the many hidden rooms before bravely going to his death.

Unfortunately for the well-intentioned Risei, said room had been designed and built by a distant predecessor to spy on the main chamber of the church. So Kyouko got the next best thing to a ringside seat view of Kayneth murdering her grandfather in cold blood.

.

Having squirreled away the barely alive Kariya Matou for later use, Kirei found his daughter weeping beside the cooling corpse of his father.

"Dad!" Kyouko latched herself around his waist. "Grandpa's dead! That man killed him!"

Kirei, too, shed tears alongside his distressed daughter. He was disappointed at having missed the chance to see his father die, just as he had watched his wife die with a beautiful smirk on her face.

Still, the salty waterworks were also the first thing he and Kyouko had truly shared. And at least he still had his daughter. She would do as a dupe for his newly-unleashed urges.

His response casually twisted the metaphysical dagger lodged in his daughter's heart. "What do you want me to do about it?" Kirei asked laconically.

She looked up to his stoic face. Her dark brown eyes overflowed with cold tears. But they also burned with innocent hate.

"I want you to find his murderer so we can kill him," Kyouko hissed.

Kirei smiled. _Perhaps she is of my flesh and blood after all._

.

Just about anyone would fall on his knees when confronted by a Heroic Spirit revealed in all his power and glory. And despite the recent horrors inflicted upon her psyche, Kyouko still retained the mind of an easily impressed child.

"Wow," the starry-eyed girl murmured, appropriately awestruck by the golden-armored King of Heroes. "You must be the most powerful hero of all time…"

Gilgamesh smirked. "I will grant you this much, Kirei," he informed his new Master. "Your child knows the proper way to regard the King of Heroes…"

.

Despite –or perhaps because of– the Black Keys embedded in his undead flesh, Zouken Matou chuckled grimly. "It seems, Kirei," the Matou hierarch commented, "That she truly is your daughter.

Kirei glanced at the defiant Kyouko. At some point in time, his daughter had filched a page of Scripture from the church or possibly his person. She then managed to transform that stolen Scripture into the Black Key currently jutting from Zouken's belly, proving that she did inherit her father's Magic Circuits and instinctively knew how to tap the power coursing through those God-given artificial veins.

"Perhaps," he allowed, deliberately letting his daughter's bosom swell with happy pride, all the better to puncture her bubble of joy at a later time.

.

"Welcome home, Kyouko."

She recognized the woman at the doorstep of the Church. Their hair shared the same sunset shade. Similar curves defined their faces into heart shapes. This was how she would look like fifteen years and two children into the future.

Kyouko remembered the sterile hospital ward. And the somber funeral. And the finely-chiseled headstone of Ashford black marble at the back of the church that set apart a particular plot.

**As the flowers are all made sweeter by ****the sunshine and the dew, so this old world is made brighter by the lives of folks like you…**

She startled at the unexpected but pleasant sensation of small fingers seizing her hands. A little girl, hair gathered up into a single tuft of pink, favored her with a huge smile.

"Come on, big sister! The shrimp is going to get cold!"

_Who are you?_

Confused, Kyouko looked to her father for an explanation. The man in the black soutane was somewhat stout and possessed a well-kept goatee rather like the aristocratic beard cultivated by Rin's dad.

"It's your turn to say grace over the meal, Kyouko," he reminded her with a small smile.

_Who are you?_

This was wrong. Her mother was dead. She was an only child; her little sister died stillborn. And this man was not her father, he was not Kirei Kotomine.

And yet…

And yet it felt right. As if it was how things should be. Here, with these people, the people who comprised her family, she was home.

So Kyouko meekly tagged after the smiling phantasms, a paschal lamb led to the slaughterhouse by a promise of paradise lost.

.

**Hope springs eternal in the human breast;**

**Man never is, but always to be blessed:**

**The soul, uneasy and confined from home,**

**Rests and expatiates in a life to come.**

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At the corner of her teary eyes, black raindrops spattered across the murky glass of the window.

Perhaps that was why they called it a windowpane.

.

Despite its corruption and incompletion, the Holy Grail could still accomplish miracles. It could torch hectares of land with the smoldering sludge of the River Styx. It could grant a corporeal body to a Heroic Spirit. It could even replace a heart destroyed by a 7.62x51 millimeter Origin Bullet.

But even the Grail wasn't capable of regenerating or replacing the brain matter splattered all over the face of the horrified Kyouko, who had been watching the epic duel of the fates between her father and Kiritsugu when the Mage Killer shifted his aim at the last second and drilled his final shot through the back of Kirei's skull, execution style.

"NOOO!"

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_They're dead. Mother. Grandfather. Dad. All of them are dead._

_I'm alone now. Forever alone._

Lazily swirling around the folded legs of the despairing girl, the blood-tainted muck from the Holy Grail pulsed.

_**What is your wish,**_ tempted Angra Mainyu.

Drenched and dripping with black mud, Kyouko hauled herself upright. She cupped her palms together, caught a double handful of cursed sludge, and raised it above her pretty head.

"Kill them," she prayed. "Kill them all."

And there was fire.

.

Kyouko came awake to find herself borne gently within strong arms.

_Father? No, he's dead… so is Grandfather and Mother… I am alone, the last of my cursed line…_

Thick mud clogged her throat. She coughed, attempting to clear her craw, then thought better of it and just swallowed. She had bathed in the distilled hate of humankind. What was a small chug or two?

She looked up at the shining face of her savior, only to avert her eyes out of honest humility.

"Gilgamesh-sama," Kyouko murmured. "Thank you for saving me…"

The King of Heroes smirked at her. "Your good manners remain in the presence of the King. We are pleased. What is your name, child of Kotomine?" he drawled.

"Kyouko,"

"Then, Kyouko Kotomine," Gilgamesh smugly proclaimed, "I will deign to consider you as my Master."

_He reminds me of my father._ _I wonder who influenced whom? Or perhaps they both benefited from each other's presence._

Carefully she considered what to say and how to phrase it. Fortunately she knew the Bible by heart. And the King James Version was sufficiently archaic and courteous for her purposes.

"With your consent, Gilgamesh-sama, I beseech thee to set me down. From here I will walk on my own two feet behind you as befits an inferior who owes her survival and continued existence to your everlasting generosity."

The amused Gilgamesh allowed his proud frame to stoop once more on behalf of a mere mortal- no, of his Master, a worthy partner.

After thanking him profusely, Kyouko examined her right hand. Glowing lines of Command Seals coursed throughout her pale skin.

"Thank you, grandfather. Your sacrifice will not be in vain…"

.

"_**God is spirit, and his worshipers must worship in spirit and in truth."**_

_The Gospel of John 4:24_

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Five years later, Shirou Emiya came to an abrupt halt, having walked into a metaphorical yet solid-seeming wall of ominous air erected by the forbidding tune of Dies Irae issuing from the serried ranks of a lovingly-maintained pipe organ.

"Rejoice, young man. Your wish will be granted."

Sister Kyouko Kotomine smirked.

.

BAD END


End file.
